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Bai WN, Wang WT, Zhang DY. Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree. Mol Phylogenet Evol 2014; 81:37-48. [DOI: 10.1016/j.ympev.2014.08.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 08/25/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
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202
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Low level of genetic divergence between Harpagifer fish species (Perciformes: Notothenioidei) suggests a Quaternary colonization of Patagonia from the Antarctic Peninsula. Polar Biol 2014. [DOI: 10.1007/s00300-014-1623-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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203
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Clouse RM, Janda M, Blanchard B, Sharma P, Hoffmann BD, Andersen AN, Czekanski-Moir JE, Krushelnycky P, Rabeling C, Wilson EO, Economo EP, Sarnat EM, General DM, Alpert GD, Wheeler WC. Molecular phylogeny of Indo-Pacific carpenter ants (Hymenoptera: Formicidae,Camponotus) reveals waves of dispersal and colonization from diverse source areas. Cladistics 2014; 31:424-437. [DOI: 10.1111/cla.12099] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
- Ronald M. Clouse
- Department of Bioinformatics and Genomics; University of North Carolina at Charlotte; 9201 University City Blvd Charlotte NC 28223 USA
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th St. New York City NY 10024 USA
| | - Milan Janda
- Biology Centre; Czech Academy of Sciences; Branisovska 31 370 05 Ceske Budejovice Czech Republic
- Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Benjamin Blanchard
- Department of Ecology and Evolutionary Biology; University of Michigan; 2019 Kraus Natural Science Building Ann Arbor MI 48109 USA
| | - Prashant Sharma
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th St. New York City NY 10024 USA
| | | | | | - Jesse E. Czekanski-Moir
- Department of Biology; Program in Ecology and Evolutionary Biology; University of Oklahoma; Norman OK 73019 USA
| | - Paul Krushelnycky
- Department of Plant and Environmental Protection Sciences; University of Hawaiʻi at Mānoa; 3050 Maile Way Room 310 Honolulu HI 96822 USA
| | - Christian Rabeling
- Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Edward O. Wilson
- Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Evan P. Economo
- Okinawa Institute of Science and Technology; 1919-1 Tancha Onna-son Kunigami gun Okinawa Japan 904-0495
| | - Eli M. Sarnat
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
| | - David M. General
- University of the Philippines at Los Baños; Museum of Natural History; Los Baños 4031 Laguna Philippines
| | - Gary D. Alpert
- Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th St. New York City NY 10024 USA
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204
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Thielsch A, Glass N, Streit B, Meester LD, Ortells R, Schwenk K. Fitness differences and persistent founder effects determine the clonal composition during population build-up inDaphnia. OIKOS 2014. [DOI: 10.1111/oik.01575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anne Thielsch
- Inst. for Environmental Science, Molecular Ecology, Univ. of Koblenz-Landau; Fortstraße 7 DE-76829 Landau Germany
| | - Nicole Glass
- Dept of Ecology and Evolution; Goethe-Univ. - Biologicum; Max-von-Laue-Straße 13 DE-60438 Frankfurt am Main Germany
| | - Bruno Streit
- Dept of Ecology and Evolution; Goethe-Univ. - Biologicum; Max-von-Laue-Straße 13 DE-60438 Frankfurt am Main Germany
| | - Luc De Meester
- Laboratory Aquatic Ecology, Evolution and Conservation, KU Leuven - Univ. of Leuven; Charles Deberiotstraat 32 BE-3000 Leuven Belgium
| | - Raquel Ortells
- Inst. Cavanilles de Biodiversitat i Biologia Evolutiva, Univ. of Valencia; C/Catedrático José Beltrán, 2 ES-46980 Paterna Spain
| | - Klaus Schwenk
- Inst. for Environmental Science, Molecular Ecology, Univ. of Koblenz-Landau; Fortstraße 7 DE-76829 Landau Germany
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205
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Hedenäs L, Bisang I. Infraspecific diversity in a spore-dispersed species with limited distribution range. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.968234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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206
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Scorched mussels (BIVALVIA: MYTILIDAE: BRACHIDONTINAE) from the temperate coasts of South America: phylogenetic relationships, trans-Pacific connections and the footprints of Quaternary glaciations. Mol Phylogenet Evol 2014; 82 Pt A:60-74. [PMID: 25451805 DOI: 10.1016/j.ympev.2014.10.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 08/26/2014] [Accepted: 10/03/2014] [Indexed: 11/22/2022]
Abstract
This study addresses aspects of the phylogeny and phylogeography of scorched mussels (BIVALVIA: MYTILIDAE: BRACHIDONTINAE) from southern South America (Argentina and Chile), as well as their ecophylogenetic implications. Relationships were inferred from sequences of two nuclear (28S and 18S) and one mitochondrial (COI) genes, using Bayesian and maximum likelihood analyses. Our results indicate that the monophyletic BRACHIDONTINAE include three well supported clades: [i] Brachidontes Swainson (=Hormomya Mörch), [ii] Ischadium Jukes-Browne+Geukensia van de Poel, and [iii] Austromytilus Laseron+Mytilisepta Habe (usually considered a member of the SEPTIFERINAE)+Perumytilus Olsson. Species of clade [iii] are distributed along the temperate coasts of the Pacific Ocean. Available evidence supports divergence between Austromytilus (Australia) and Perumytilus (South American) following the breakup of Australian, Antarctic and South American shelves. Four brachidontins occur in southern South America: Brachidontes rodriguezii (d'Orbigny), B. granulatus (Hanley), and two genetically distinct clades of Perumytilus. The latter are confined to the Chile-Peru (North Clade) and Magellanic (South Clade) Biogeographic Provinces, respectively warm- and cold-temperate. The South Clade is the only brachidontin restricted to cold-temperate waters. Biogeographic considerations and the fossil record prompted the hypothesis that the South Clade originated from the North Clade by incipient peripatric differentiation, followed by isolation during the Quaternary glaciations, genetic differentiation in the non-glaciated coasts of eastern Patagonia, back-expansion over southern Chile following post-LGM de-glaciation, and development of a secondary contact zone between the two clades in south-central Chile. Evidence of upper Pleistocene expansion of the South Clade parallels similar results on other organisms that have colonized coastal ecosystems from eastern Patagonia since the LGM, apparently occupying free ecological space. We emphasize that the assembly of communities cannot be explained solely in terms of environmental drivers, as history also matters.
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207
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Kraft B, Tegetmeyer HE, Meier D, Geelhoed JS, Strous M. Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture. Environ Microbiol 2014; 16:3275-86. [PMID: 24976559 DOI: 10.1111/1462-2920.12552] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/19/2014] [Indexed: 02/02/2023]
Abstract
Marine denitrification constitutes an important part of the global nitrogen cycle and the diversity, abundance and process rates of denitrifying microorganisms have been the focus of many studies. Still, there is little insight in the ecophysiology of marine denitrifying communities. In this study, a heterotrophic denitrifying community from sediments of a marine intertidal flat active in nitrogen cycling was selected in a chemostat and monitored over a period of 50 days. The chemostat enabled the maintenance of constant and well-defined experimental conditions over the time-course of the experiment. Analysis of the microbial community composition by automated ribosomal intergenic spacer analysis (ARISA), Illumina sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed strong dynamics in community composition over time, while overall denitrification by the enrichment culture was stable. Members of the genera Arcobacter, Pseudomonas, Pseudovibrio, Rhodobacterales and of the phylum Bacteroidetes were identified as the dominant denitrifiers. Among the fermenting organisms co-enriched with the denitrifiers was a novel archaeon affiliated with the recently proposed DPANN-superphylum. The pan-genome of populations affiliated to Pseudovibrio encoded a NirK as well as a NirS nitrite reductase, indicating the rare co-occurrence of both evolutionary unrelated nitrite reductases within coexisting subpopulations.
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Affiliation(s)
- Beate Kraft
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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208
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Aranda SC, Gabriel R, Borges PAV, Santos AMC, de Azevedo EB, Patiño J, Hortal J, Lobo JM. Geographical, temporal and environmental determinants of bryophyte species richness in the Macaronesian islands. PLoS One 2014; 9:e101786. [PMID: 25003186 PMCID: PMC4086965 DOI: 10.1371/journal.pone.0101786] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/11/2014] [Indexed: 11/18/2022] Open
Abstract
Species richness on oceanic islands has been related to a series of ecological factors including island size and isolation (i.e. the Equilibrium Model of Island Biogeography, EMIB), habitat diversity, climate (i.e., temperature and precipitation) and more recently island ontogeny (i.e. the General Dynamic Model of oceanic island biogeography, GDM). Here we evaluate the relationship of these factors with the diversity of bryophytes in the Macaronesian region (Azores, Madeira, Canary Islands and Cape Verde). The predictive power of EMIB, habitat diversity, climate and the GDM on total bryophyte richness, as well as moss and liverwort richness (the two dominant bryophyte groups), was evaluated through ordinary least squares regressions. After choosing the best subset of variables using inference statistics, we used partial regression analyses to identify the independent and shared effects of each model. The variables included within each model were similar for mosses and liverworts, with orographic mist layer being one of the most important predictors of richness. Models combining climate with either the GDM or habitat diversity explained most of richness variation (up to 91%). There was a high portion of shared variance between all pairwise combinations of factors in mosses, while in liverworts around half of the variability in species richness was accounted for exclusively by climate. Our results suggest that the effects of climate and habitat are strong and prevalent in this region, while geographical factors have limited influence on Macaronesian bryophyte diversity. Although climate is of great importance for liverwort richness, in mosses its effect is similar to or, at least, indiscernible from the effect of habitat diversity and, strikingly, the effect of island ontogeny. These results indicate that for highly vagile taxa on oceanic islands, the dispersal process may be less important for successful colonization than the availability of suitable ecological conditions during the establishment phase.
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Affiliation(s)
- Silvia C. Aranda
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Madrid, Spain
- Azorean Biodiversity Group and Platform for Enhancing Ecological Research & Sustainability, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
- * E-mail:
| | - Rosalina Gabriel
- Azorean Biodiversity Group and Platform for Enhancing Ecological Research & Sustainability, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Paulo A. V. Borges
- Azorean Biodiversity Group and Platform for Enhancing Ecological Research & Sustainability, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Ana M. C. Santos
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Madrid, Spain
- Azorean Biodiversity Group and Platform for Enhancing Ecological Research & Sustainability, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
- Centro de Biologia Ambiental and Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Eduardo Brito de Azevedo
- Centro do Clima, Meteorologia e Mudanças Globais, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - Jairo Patiño
- Azorean Biodiversity Group and Platform for Enhancing Ecological Research & Sustainability, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
- Institute of Botany, University of Liège, Liège, Belgium
- Departmento de Biología Vegetal, Universidad de La Laguna, Tenerife, Spain
| | - Joaquín Hortal
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Madrid, Spain
- Centro de Biologia Ambiental and Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Jorge M. Lobo
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Madrid, Spain
- Azorean Biodiversity Group and Platform for Enhancing Ecological Research & Sustainability, Departamento de Ciências Agrárias, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
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209
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Collins CJ, Rawlence NJ, Prost S, Anderson CNK, Knapp M, Scofield RP, Robertson BC, Smith I, Matisoo-Smith EA, Chilvers BL, Waters JM. Extinction and recolonization of coastal megafauna following human arrival in New Zealand. Proc Biol Sci 2014; 281:20140097. [PMID: 24827440 PMCID: PMC4046402 DOI: 10.1098/rspb.2014.0097] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/14/2014] [Indexed: 11/12/2022] Open
Abstract
Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction-replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.
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Affiliation(s)
- Catherine J Collins
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Nicolas J Rawlence
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Stefan Prost
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin 9016, New Zealand Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | | | - Michael Knapp
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin 9016, New Zealand School of Biological Sciences, Bangor University, Bangor, LL57 2UW, Wales, UK
| | | | - Bruce C Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Ian Smith
- Department of Anthropology and Archaeology, University of Otago, Dunedin 9016, New Zealand
| | - Elizabeth A Matisoo-Smith
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - B Louise Chilvers
- Department of Conservation, Marine Species and Threats, Wellington 6011, New Zealand
| | - Jonathan M Waters
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand
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210
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Ranjard L, Welch D, Paturel M, Guindon S. Modelling Competition and Dispersal in a Statistical Phylogeographic Framework. Syst Biol 2014; 63:743-52. [DOI: 10.1093/sysbio/syu040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Louis Ranjard
- Bioinformatics Institute; 2Department of Computer Sciences; 3Department of Statistics, The University of Auckland, New Zealand and 4LIRMM, CNRS, Montpellier, France
| | - David Welch
- Bioinformatics Institute; 2Department of Computer Sciences; 3Department of Statistics, The University of Auckland, New Zealand and 4LIRMM, CNRS, Montpellier, France
| | - Marie Paturel
- Bioinformatics Institute; 2Department of Computer Sciences; 3Department of Statistics, The University of Auckland, New Zealand and 4LIRMM, CNRS, Montpellier, France
| | - Stéphane Guindon
- Bioinformatics Institute; 2Department of Computer Sciences; 3Department of Statistics, The University of Auckland, New Zealand and 4LIRMM, CNRS, Montpellier, France
- Bioinformatics Institute; 2Department of Computer Sciences; 3Department of Statistics, The University of Auckland, New Zealand and 4LIRMM, CNRS, Montpellier, France
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211
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212
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Eschbach E, Nolte AW, Kohlmann K, Kersten P, Kail J, Arlinghaus R. Population differentiation of zander (Sander lucioperca) across native and newly colonized ranges suggests increasing admixture in the course of an invasion. Evol Appl 2014; 7:555-68. [PMID: 24944569 PMCID: PMC4055177 DOI: 10.1111/eva.12155] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/21/2014] [Indexed: 11/29/2022] Open
Abstract
In addition to ecological factors, evolutionary processes can determine the invasion success of a species. In particular, genetic admixture has the potential to induce rapid evolutionary change, which can result from natural or human-assisted secondary contact between differentiated populations. We studied the recent range expansion of zander in Germany focusing on the interplay between invasion and genetic admixture. Historically, the rivers Elbe and Danube harboured the most north-western source populations from which a north-westward range expansion occurred. This was initiated by introducing zander outside its native range into rivers and lakes, and was fostered by migration through artificial canals and stocking from various sources. We analysed zander populations of the native and invaded ranges using nuclear and mitochondrial genetic markers. Three genetic lineages were identified, which were traced to ancestral ranges. Increased genetic diversity and admixture in the invaded region highlighted asymmetric gene flow towards this area. We suppose that the adaptive potential of the invading populations was promoted by genetic admixture, whereas competitive exclusion in the native areas provided a buffer against introgression by novel genotypes. These explanations would be in line with evidence that hybridization can drive evolutionary change under conditions when new niches can be exploited.
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Affiliation(s)
- Erik Eschbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Germany
| | - Arne W Nolte
- Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Klaus Kohlmann
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Germany
| | - Petra Kersten
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Germany
| | - Jochem Kail
- Department of Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen Essen, Germany
| | - Robert Arlinghaus
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Germany ; Chair of Integrative Fisheries Management, Faculty of Agriculture and Horticulture, Humboldt-Universität zu Berlin Berlin, Germany
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213
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Leys M, Petit EJ, El-Bahloul Y, Liso C, Fournet S, Arnaud JF. Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes. Ecol Evol 2014; 4:1828-52. [PMID: 24963380 PMCID: PMC4063479 DOI: 10.1002/ece3.1061] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 11/25/2022] Open
Abstract
Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity.
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Affiliation(s)
- Marie Leys
- Laboratoire de Génétique et Évolution des Populations Végétales, UMR CNRS 8198, Bâtiment SN2, Université des Sciences et Technologies de Lille - Lille 1 Villeneuve d'Ascq Cedex, F-59655, France
| | - Eric J Petit
- UMR CNRS 6553 ECOBIO, Station biologique, Université de Rennes 1 Paimpont, F-35380, France
| | - Yasmina El-Bahloul
- Unité d'Amélioration des Plantes Conservation et Valorisation des Ressources Phytogénétiques, Centre Régional de la Recherche Agronomique de Rabat, INRA-Maroc Rabat-Instituts, 10101, Morocco
| | - Camille Liso
- Laboratoire de Génétique et Évolution des Populations Végétales, UMR CNRS 8198, Bâtiment SN2, Université des Sciences et Technologies de Lille - Lille 1 Villeneuve d'Ascq Cedex, F-59655, France
| | - Sylvain Fournet
- UMR 1349 IGEPP, INRA - Agrocampus Ouest-Université de Rennes 1 Bât 320, BP35327, Le Rheu Cedex, 35653, France
| | - Jean-François Arnaud
- Laboratoire de Génétique et Évolution des Populations Végétales, UMR CNRS 8198, Bâtiment SN2, Université des Sciences et Technologies de Lille - Lille 1 Villeneuve d'Ascq Cedex, F-59655, France
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214
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Zhang ZY, Cashins S, Philips A, Burridge CP. Significant population genetic structuring but a lack of phylogeographic structuring in the endemic Tasmanian tree frog (Litoria burrowsae). AUST J ZOOL 2014. [DOI: 10.1071/zo14028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conservation of frogs is of global concern, owing to declines resulting from habitat destruction, global climate change, and disease. Knowledge of genetic variation in frog species is therefore desirable for the identification of management units. Here we surveyed mitochondrial DNA sequence variation in the Tasmanian endemic hylid frog Litoria burrowsae, which is infected by chytrid fungus, Batrachochytrium dendrobatidis, and may be declining. Neither phylogeographic structure nor deep phylogenetic divergence was detected in the species, although its populations were highly differentiated with respect to haplotype frequencies. The low-haplotype diversity in L. burrowsae suggests a recent bottleneck in the species, and population genetic structuring may reflect isolation by distance as well as founder effects associated with range expansion. Three putative management units were identified that require verification based on nuclear DNA variation and adaptation to local environments.
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215
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King RA, Leys R. Molecular evidence for mid-Pleistocene divergence of populations of three freshwater amphipod species (Talitroidea : Chiltoniidae) on Kangaroo Island, South Australia, with a new spring-associated genus and species. AUST J ZOOL 2014. [DOI: 10.1071/zo13099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent molecular and morphological analyses have shown that chiltoniid amphipods, once thought to be a relictual group, are a diverse and speciose family of Australian freshwater amphipods. As part of a larger examination of the family, chiltoniids from Kangaroo Island in South Australia were collected and analysed using molecular (COI and 28S) and morphological methods in order to understand species distributional patterns and relationships. Kartachiltonia moodyi gen. nov., sp. nov., a spring-associated species endemic to the island, was discovered and populations of three additional mainland species (Austrochiltonia australis, A. dalhousiensis and A. subtenuis) were examined. The island populations of A. australis, A. dalhousiensis and A. subtenuis were found to form natural groups with differing haplotype coalescence times dating from the Early to Mid-Pleistocene. Numerous cycles of regional climate change throughout the Pleistocene are likely to have driven speciation in chiltoniid amphipods in southern Australia and the presence of multiple chiltoniid species at Kangaroo Island indicates that it exists at a likely convergence of species distribution patterns. Three possible hypotheses to explain the evolution and diversity of chiltoniids in southern Australia are discussed as are evidence for potential introduction and long-distance dispersal events.
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216
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Star B, Haverkamp THA, Jentoft S, Jakobsen KS. Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location. BMC Microbiol 2013; 13:248. [PMID: 24206635 PMCID: PMC3840566 DOI: 10.1186/1471-2180-13-248] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 11/07/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The observation that specific members of the microbial intestinal community can be shared among vertebrate hosts has promoted the concept of a core microbiota whose composition is determined by host-specific selection. Most studies investigating this concept in individual hosts have focused on mammals, yet the diversity of fish lineages provides unique comparative opportunities from an evolutionary, immunological and environmental perspective. Here we describe microbial intestinal communities of eleven individual Atlantic cod (Gadus morhua) caught at a single location based on an extensively 454 sequenced 16S rRNA library of the V3 region. RESULTS We obtained a total of 280447 sequences and identify 573 Operational Taxonomic Units (OTUs) at 97% sequence similarity level, ranging from 40 to 228 OTUs per individual. We find that ten OTUs are shared, though the number of reads of these OTUs is highly variable. This variation is further illustrated by community diversity estimates that fluctuate several orders of magnitude among specimens. The shared OTUs belong to the orders of Vibrionales, which quantitatively dominate the Atlantic cod intestinal microbiota, followed by variable numbers of Bacteroidales, Erysipelotrichales, Clostridiales, Alteromonadales and Deferribacterales. CONCLUSIONS The microbial intestinal community composition varies significantly in individual Atlantic cod specimens caught at a single location. This high variation among specimens suggests that a complex combination of factors influence the species distribution of these intestinal communities.
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Affiliation(s)
- Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway.
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Defaveri J, Shikano T, Shimada Y, Merilä J. High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus). Mol Ecol 2013; 22:4811-28. [PMID: 23947683 DOI: 10.1111/mec.12430] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 06/11/2013] [Accepted: 06/18/2013] [Indexed: 12/12/2022]
Abstract
Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene-based genome-scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection-as determined with several outlier detection methods-was low (F(ST) = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (F(ST) = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.
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Affiliation(s)
- Jacquelin Defaveri
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
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218
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Fraser CI, Zuccarello GC, Spencer HG, Salvatore LC, Garcia GR, Waters JM. Genetic affinities between trans-oceanic populations of non-buoyant macroalgae in the high latitudes of the Southern Hemisphere. PLoS One 2013; 8:e69138. [PMID: 23894421 PMCID: PMC3718832 DOI: 10.1371/journal.pone.0069138] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships – even shared haplotypes – were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.
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Affiliation(s)
- Ceridwen I Fraser
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand.
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219
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White TA, Perkins SE, Heckel G, Searle JB. Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland. Mol Ecol 2013; 22:2971-85. [PMID: 23701376 DOI: 10.1111/mec.12343] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/03/2013] [Indexed: 12/17/2022]
Abstract
Range expansions are extremely common, but have only recently begun to attract attention in terms of their genetic consequences. As populations expand, demes at the wave front experience strong genetic drift, which is expected to reduce genetic diversity and potentially cause 'allele surfing', where alleles may become fixed over a wide geographical area even if their effects are deleterious. Previous simulation models show that range expansions can generate very strong selective gradients on dispersal, reproduction, competition and immunity. To investigate the effects of range expansion on genetic diversity and adaptation, we studied the population genomics of the bank vole (Myodes glareolus) in Ireland. The bank vole was likely introduced in the late 1920s and is expanding its range at a rate of ~2.5 km/year. Using genotyping-by-sequencing, we genotyped 281 bank voles at 5979 SNP loci. Fourteen sample sites were arranged in three transects running from the introduction site to the wave front of the expansion. We found significant declines in genetic diversity along all three transects. However, there was no evidence that sites at the wave front had accumulated more deleterious mutations. We looked for outlier loci with strong correlations between allele frequency and distance from the introduction site, where the direction of correlation was the same in all three transects. Amongst these outliers, we found significant enrichment for genic SNPs, suggesting the action of selection. Candidates for selection included several genes with immunological functions and several genes that could influence behaviour.
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Affiliation(s)
- Thomas A White
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853-2701, USA.
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220
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Coleman MA. Connectivity of the habitat-forming kelp, Ecklonia radiata within and among estuaries and open coast. PLoS One 2013; 8:e64667. [PMID: 23717648 PMCID: PMC3662792 DOI: 10.1371/journal.pone.0064667] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
With marine protected areas being established worldwide there is a pressing need to understand how the physical setting in which these areas are placed influences patterns of dispersal and connectivity of important marine organisms. This is particularly critical for dynamic and complex nearshore marine environments where patterns of genetic structure of organisms are often chaotic and uncoupled from broad scale physical processes. This study determines the influence of habitat heterogeneity (presence of estuaries) on patterns of genetic structure and connectivity of the common kelp, Ecklonia radiata. There was no genetic differentiation of kelp between estuaries and the open coast and the presence of estuaries did not increase genetic differentiation among open coast populations. Similarly, there were no differences in level of inbreeding or genetic diversity between estuarine and open coast populations. The presence of large estuaries along rocky coastlines does not appear to influence genetic structure of this kelp and factors other than physical heterogeneity of habitat are likely more important determinants of regional connectivity. Marine reserves are currently lacking in this bioregion and may be designated in the future. Knowledge of the factors that influence important habitat forming organisms such as kelp contribute to informed and effective marine protected area design and conservation initiatives to maintain resilience of important marine habitats.
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Affiliation(s)
- Melinda A Coleman
- Centre for Marine BioInnovation, University of New South Wales, Sydney, New South Wales, Australia.
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Godfrey M Hewitt (1940-2013): highlights in Heredity from a career in evolutionary genetics. Heredity (Edinb) 2013; 110:405-6. [PMID: 23591550 DOI: 10.1038/hdy.2013.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
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222
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Buckley HL, Paterson AM, Cruickshank RH. The founder space race: a response to Waters et al. Trends Ecol Evol 2013; 28:189-90. [DOI: 10.1016/j.tree.2013.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/06/2013] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
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223
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The founder space race: a reply to Buckley et al. Trends Ecol Evol 2013; 28:190-1. [DOI: 10.1016/j.tree.2013.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/14/2013] [Accepted: 01/14/2013] [Indexed: 11/20/2022]
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224
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Waters JM, Trewick SA, Paterson AM, Spencer HG, Kennedy M, Craw D, Burridge CP, Wallis GP. Biogeography Off the Tracks. Syst Biol 2013; 62:494-8. [DOI: 10.1093/sysbio/syt013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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225
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Bisconti R, Canestrelli D, Nascetti G. Has living on islands been so simple? Insights from the insular endemic frog Discoglossus montalentii. PLoS One 2013; 8:e55735. [PMID: 23393599 PMCID: PMC3564813 DOI: 10.1371/journal.pone.0055735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/30/2012] [Indexed: 11/21/2022] Open
Abstract
Island populations have been extensively used as model systems in ecology, biogeography, conservation and evolutionary biology, owing to the several simplifying assumptions that they allow. Nevertheless, recent findings from intra-island phylogeographic studies are casting doubts on the generality of some of these underlying assumptions. We investigated the phylogeography, historical demography, and population genetic structure of the Corsican endemic frog, Discoglossus montalentii. In contrast with expectations based on its insular, restricted and continuous distribution, we found evidence of 3 phylogroups, whose rather ancient divergence (Early-Middle Pleistocene) was likely primed by climatic changes that occurred during the ‘middle Pleistocene revolution’. Furthermore, their differentiation explained most (68%) of the overall genetic diversity that was observed. These results and the growing evidence from intra-island phylogeographies, suggest that island populations frequently may not conform to some long-standing assumptions, including long-term stability, range-wide panmixia and the correlation of effective population size to the island size. As a consequence, both for theoretical and for applied purposes, the extensive use of these assumptions in the study of island populations warrants a careful re-examination.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
- * E-mail:
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
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